6-Amino-2-iminiumyl-4-oxo-1,2,3,4-tetra­hydro­pyrimidin-5-aminium sulfate monohydrate

The title compound, C₄H₉N₅O²⁺·SO₄²⁻·H₂O, is the monohydrate of the commercially available compound `C₄H₇N₅O·H₂SO₄·xH₂O'. It is obtained by reprecipitation of C₄H₇N₅O·H₂SO₄·xH₂O from dilute sodium hydroxide solution with dilute sulfuric acid. The crystal structure of anhydrous 2,4,5-tri­amino-1,6-di­hydro­pyrimidin-6-one sulfate is known, although called by the authors 5-amminium-6-amino-isocytosinium sulfate [Bieri et al. (1993). Private communication (refcode HACDEU). CCDC, Cambridge, England]. In the structure, the sulfate group is deprotonated, whereas one of the amino groups is protonated (R₂C—NH₃⁺) and one is rearranged to a protonated imine group (R₂C=NH₂⁺). This arrangement is very similar to the known crystal structure of the anhydrate. Several tautomeric forms of the investigated mol­ecule are possible, which leads to questionable proton attributions. The measured data allowed the location of all hydrogen atoms from the residual electron density. In the crystal, ions and water mol­ecules are linked into a three-dimensional network by N—H...O and O—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.080
• wR factor = 0.281
• Data-to-parameter ratio = 9.6

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT417_ALERT_2_B Short Inter D-H..H-D       Hw11     ..Hw11     .       1.94 Ang.
                                                 2-x,1-y,-z  =      2_765 Check

Author Response: Possibly incorrect or disordered orientation of the water molecule. Precision limited by crystal quality.

Alert level C
PLAT018_ALERT_1_C _diffrn_measured_fraction_theta_max .NE. *_full           ! Check
PLAT084_ALERT_3_C High wR2 Value (i.e. > 0.25) ...................       0.28 Report
PLAT088_ALERT_3_C Poor Data / Parameter Ratio ....................       9.61 Note
PLAT230_ALERT_2_C Hirshfeld Test Diff for    N13      --C12      .        6.0 s.u.
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............     0.0055 Ang.
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600         79 Report
PLAT975_ALERT_2_C Check Calcd Resid. Dens.  1.00A   From O3              0.43 eA-3
PLAT975_ALERT_2_C Check Calcd Resid. Dens.  1.08A   From N8              0.42 eA-3
PLAT976_ALERT_2_C Check Calcd Resid. Dens.  0.91A   From Ow1            -0.60 eA-3
PLAT976_ALERT_2_C Check Calcd Resid. Dens.  0.92A   From N11            -0.59 eA-3
PLAT976_ALERT_2_C Check Calcd Resid. Dens.  0.67A   From O3             -0.43 eA-3
PLAT976_ALERT_2_C Check Calcd Resid. Dens.  0.85A   From N13            -0.42 eA-3
PLAT976_ALERT_2_C Check Calcd Resid. Dens.  0.91A   From O4             -0.42 eA-3
PLAT978_ALERT_2_C Number C-C Bonds with Positive Residual Density.          0 Info

Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite         13 Note
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          3 Report
PLAT072_ALERT_2_G SHELXL First  Parameter in WGHT  Unusually Large       0.20 Report
PLAT154_ALERT_1_G The s.u.'s on the Cell Angles are Equal ..(Note)      0.004 Degree
PLAT172_ALERT_4_G The CIF-Embedded .res File Contains DFIX Records          3 Report
PLAT173_ALERT_4_G The CIF-Embedded .res File Contains DANG Records          2 Report
PLAT174_ALERT_4_G The CIF-Embedded .res File Contains FLAT Records          1 Report
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          3 Note
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............         20 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         56 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
  14 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  10 ALERT level G = General information/check it is not something unexpected

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
  12 ALERT type 2 Indicator that the structure model may be wrong or deficient
   5 ALERT type 3 Indicator that the structure quality may be low
   5 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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Computing details

Data collection: APEX3 (Bruker, 2012); cell refinement: SAINT (Bruker, 2015); data reduction: SAINT (Bruker, 2015); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2008) and ORTEPIII (Burnett & Johnson, 1996); software used to prepare material for publication: publCIF (Westrip, 2010).

6-Amino-2-iminiumyl-4-oxo-1,2,3,4-tetrahydropyrimidin-5-aminium sulfate monohydrate

Crystal data

C4H9N5O^2+·SO4^2^−·H2O	Z = 2
Mr = 257.24	F(000) = 268
Triclinic, P1	Dx = 1.778 Mg m^−3
a = 7.0128 (7) Å	Cu Kα radiation, λ = 1.54178 Å
b = 7.9882 (8) Å	Cell parameters from 9522 reflections
c = 9.0732 (9) Å	θ = 2.5–69.4°
α = 74.121 (4)°	µ = 3.34 mm^−1
β = 86.734 (4)°	T = 296 K
γ = 79.290 (4)°	Block, pale yellow
V = 480.36 (8) Å^3	0.2 × 0.15 × 0.1 mm

Data collection

Siemens Bruker CCD diffractometer	1599 reflections with I > 2σ(I)
Radiation source: microfocus tube	Rint = 0.051
ω and Phi scans	θmax = 71.1°, θmin = 5.1°
Absorption correction: multi-scan (SADABS; Bruker, 2015)	h = −8→8
Tmin = 0.526, Tmax = 0.753	k = −9→9
20827 measured reflections	l = −10→10
1720 independent reflections

Refinement

Refinement on F^2	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.080	w = 1/[σ^2(Fo^2) + (0.2P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.281	(Δ/σ)max = 0.002
S = 1.40	Δρmax = 0.63 e Å^−3
1720 reflections	Δρmin = −1.04 e Å^−3
179 parameters	Extinction correction: SHELXL2018 (Sheldrick, 2015b), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
20 restraints	Extinction coefficient: 0.081 (15)

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. All H atoms could be located by difference Fourier synthesis. Subsequently, H atoms bound to N atoms were refined using a riding model with the amino N–H distances constrained to 0.85 Å and the imino N–H distances constrained to 0.88 Å. For the H atoms of the amino groups, free rotation about their local threefold axis was allowed and their isotropic displacement parameters were set to U_iso(H) = 1.5U_eq(N). The coordinates of the H atoms of the water molecules were refined with the O–H distances restrained to 0.84 (1) Å and the H–H distance restrained to 1.4 (1) Å. Their isotropic displacement parameters were coupled to the equivalent isotropic displacement parameters of the O atoms, with U_iso(H) = 1.2U_eq(O).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
S1	0.29190 (9)	0.72804 (10)	0.15928 (8)	0.0303 (6)
O2	0.3943 (4)	0.5471 (3)	0.1724 (3)	0.0397 (8)
O3	0.4276 (3)	0.8537 (4)	0.1119 (3)	0.0389 (8)
O4	0.2063 (4)	0.7360 (4)	0.3111 (3)	0.0430 (8)
O5	0.1362 (4)	0.7771 (4)	0.0452 (3)	0.0418 (8)
O6	0.2171 (5)	−0.1764 (4)	0.6728 (3)	0.0520 (9)
N8	0.2102 (4)	0.0973 (4)	0.8136 (3)	0.0338 (8)
H8A	0.098160	0.160461	0.833726	0.051*
H8B	0.307806	0.133069	0.847810	0.051*
H8C	0.211936	−0.016627	0.859976	0.051*
N9	0.2573 (4)	0.0009 (4)	0.4352 (3)	0.0354 (8)
H9	0.237 (4)	−0.085 (5)	0.410 (4)	0.028 (10)*
N10	0.2669 (4)	0.2969 (4)	0.3967 (3)	0.0369 (8)
H10	0.2779 (14)	0.401 (6)	0.335 (6)	0.076 (17)*
N11	0.2988 (6)	0.1773 (6)	0.1914 (4)	0.0481 (10)
H11A	0.325 (7)	0.261 (8)	0.128 (6)	0.055 (15)*
H11B	0.325 (7)	0.092 (7)	0.143 (6)	0.053 (14)*
C12	0.2422 (5)	0.2849 (5)	0.5513 (4)	0.0340 (9)
N13	0.2327 (5)	0.4357 (4)	0.5902 (4)	0.0412 (9)
H13A	0.200 (8)	0.434 (8)	0.697 (7)	0.073 (17)*
H13B	0.225 (7)	0.546 (7)	0.525 (6)	0.054 (13)*
C14	0.2309 (4)	0.1216 (5)	0.6496 (4)	0.0310 (9)
C15	0.2338 (5)	−0.0280 (5)	0.5956 (4)	0.0348 (9)
C16	0.2728 (5)	0.1591 (5)	0.3394 (4)	0.0353 (9)
OW1	0.7873 (5)	0.5365 (4)	0.0944 (3)	0.0496 (9)
HW12	0.687 (8)	0.467 (8)	0.119 (11)	0.16 (4)*
HW11	0.916 (4)	0.473 (7)	0.089 (8)	0.11 (2)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0287 (8)	0.0328 (8)	0.0267 (8)	−0.0044 (5)	0.0017 (4)	−0.0048 (5)
O2	0.0407 (14)	0.0326 (15)	0.0406 (14)	−0.0032 (11)	0.0047 (10)	−0.0041 (11)
O3	0.0345 (13)	0.0414 (15)	0.0413 (15)	−0.0126 (11)	0.0060 (11)	−0.0094 (11)
O4	0.0493 (16)	0.0475 (17)	0.0340 (14)	−0.0118 (12)	0.0090 (12)	−0.0135 (13)
O5	0.0341 (13)	0.0532 (18)	0.0351 (14)	−0.0035 (11)	−0.0040 (10)	−0.0090 (12)
O6	0.075 (2)	0.0427 (18)	0.0351 (15)	−0.0137 (15)	0.0071 (13)	−0.0042 (13)
N8	0.0305 (14)	0.0418 (18)	0.0259 (15)	−0.0051 (12)	−0.0006 (11)	−0.0046 (13)
N9	0.0453 (16)	0.0334 (18)	0.0261 (16)	−0.0069 (13)	0.0025 (12)	−0.0063 (13)
N10	0.0466 (17)	0.0348 (18)	0.0274 (16)	−0.0073 (13)	0.0027 (12)	−0.0056 (13)
N11	0.070 (2)	0.043 (2)	0.0274 (16)	−0.0072 (17)	0.0056 (15)	−0.0061 (17)
C12	0.0307 (15)	0.040 (2)	0.0272 (17)	−0.0040 (14)	0.0026 (13)	−0.0050 (15)
N13	0.061 (2)	0.0304 (18)	0.0309 (16)	−0.0055 (14)	0.0007 (14)	−0.0073 (13)
C14	0.0297 (15)	0.0329 (19)	0.0258 (17)	−0.0026 (13)	−0.0013 (12)	−0.0018 (14)
C15	0.0351 (16)	0.035 (2)	0.0270 (17)	0.0000 (14)	−0.0019 (13)	0.0009 (14)
C16	0.0362 (17)	0.040 (2)	0.0274 (16)	−0.0037 (14)	0.0023 (13)	−0.0074 (15)
OW1	0.0542 (18)	0.0508 (19)	0.0437 (17)	−0.0107 (14)	0.0046 (14)	−0.0125 (14)

Geometric parameters (Å, º)

S1—O2	1.466 (3)	N10—C12	1.382 (4)
S1—O5	1.471 (2)	N10—H10	0.88 (4)
S1—O3	1.473 (2)	N11—C16	1.316 (5)
S1—O4	1.484 (3)	N11—H11A	0.80 (6)
O6—C15	1.223 (5)	N11—H11B	0.89 (5)
N8—C14	1.449 (4)	C12—N13	1.335 (5)
N8—H8A	0.8900	C12—C14	1.377 (5)
N8—H8B	0.8900	N13—H13A	0.98 (6)
N8—H8C	0.8900	N13—H13B	0.91 (5)
N9—C16	1.343 (5)	C14—C15	1.407 (5)
N9—C15	1.415 (4)	OW1—HW12	0.953 (10)
N9—H9	0.82 (3)	OW1—HW11	0.954 (10)
N10—C16	1.333 (5)
O2—S1—O5	110.53 (16)	C16—N11—H11B	128 (3)
O2—S1—O3	110.29 (15)	H11A—N11—H11B	102 (5)
O5—S1—O3	108.68 (14)	N13—C12—C14	126.4 (3)
O2—S1—O4	108.20 (15)	N13—C12—N10	115.6 (3)
O5—S1—O4	109.32 (14)	C14—C12—N10	118.0 (3)
O3—S1—O4	109.81 (14)	C12—N13—H13A	117 (4)
C14—N8—H8A	109.5	C12—N13—H13B	126 (3)
C14—N8—H8B	109.5	H13A—N13—H13B	115 (4)
H8A—N8—H8B	109.5	C12—C14—C15	121.8 (3)
C14—N8—H8C	109.5	C12—C14—N8	121.3 (3)
H8A—N8—H8C	109.5	C15—C14—N8	116.9 (3)
H8B—N8—H8C	109.5	O6—C15—C14	126.6 (3)
C16—N9—C15	123.3 (3)	O6—C15—N9	118.4 (3)
C16—N9—H9	125 (3)	C14—C15—N9	115.0 (3)
C15—N9—H9	110 (3)	N11—C16—N10	120.3 (4)
C16—N10—C12	122.8 (3)	N11—C16—N9	120.6 (4)
C16—N10—H10	120 (4)	N10—C16—N9	119.0 (3)
C12—N10—H10	117 (4)	HW12—OW1—HW11	116 (5)
C16—N11—H11A	128 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N8—H8A···O4^i	0.89	2.46	3.113 (4)	131
N8—H8A···O5^i	0.89	1.99	2.827 (4)	157
N8—H8B···O3^ii	0.89	1.94	2.788 (4)	159
N8—H8C···O5^iii	0.89	2.13	2.942 (4)	152
N9—H9···O4^iv	0.82 (4)	1.93 (4)	2.739 (5)	168 (4)
N10—H10···O2	0.88 (4)	1.87 (4)	2.677 (4)	152 (3)
N10—H10···O4	0.88 (4)	2.58 (5)	3.329 (4)	143 (4)
N11—H11A···O2	0.80 (5)	2.56 (7)	3.106 (6)	126 (5)
N11—H11A···OW1^v	0.80 (5)	2.29 (5)	2.956 (4)	142 (5)
N11—H11B···O3^iv	0.89 (6)	2.00 (6)	2.845 (6)	158 (5)
N13—H13A···OW1^ii	0.98 (6)	1.98 (7)	2.924 (5)	161 (5)
N13—H13B···O4	0.91 (5)	2.10 (5)	2.961 (4)	156 (5)
OW1—HW12···O2	0.96 (6)	2.10 (6)	2.798 (4)	128 (5)
OW1—HW11···OW1^vi	0.96 (3)	2.59 (5)	3.390 (5)	141 (3)

Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x+1, −y+1, −z+1; (iii) x, y−1, z+1; (iv) x, y−1, z; (v) −x+1, −y+1, −z; (vi) −x+2, −y+1, −z.